ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets

Abstract ANISEED (www.aniseed.cnrs.fr) is the main model organism database for tunicates, the sister-group of vertebrates. This release gives access to annotated genomes, gene expression patterns, and anatomical descriptions for nine ascidian species. It provides increased integration with external...

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Vydáno v:	Nucleic acids research Ročník 46; číslo D1; s. D718 - D725
Hlavní autoři:	Brozovic, Matija, Dantec, Christelle, Dardaillon, Justine, Dauga, Delphine, Faure, Emmanuel, Gineste, Mathieu, Louis, Alexandra, Naville, Magali, Nitta, Kazuhiro R, Piette, Jacques, Reeves, Wendy, Scornavacca, Céline, Simion, Paul, Vincentelli, Renaud, Bellec, Maelle, Aicha, Sameh Ben, Fagotto, Marie, Guéroult-Bellone, Marion, Haeussler, Maximilian, Jacox, Edwin, Lowe, Elijah K, Mendez, Mickael, Roberge, Alexis, Stolfi, Alberto, Yokomori, Rui, Brown, C Titus, Cambillau, Christian, Christiaen, Lionel, Delsuc, Frédéric, Douzery, Emmanuel, Dumollard, Rémi, Kusakabe, Takehiro, Nakai, Kenta, Nishida, Hiroki, Satou, Yutaka, Swalla, Billie, Veeman, Michael, Volff, Jean-Nicolas, Lemaire, Patrick
Médium:	Journal Article
Jazyk:	angličtina
Vydáno:	England Oxford University Press 04.01.2018
Témata:	Animals Biological Evolution Ciona intestinalis - genetics Computer Science Data Mining Database Issue Databases, Genetic Datasets as Topic DNA - metabolism Evolution, Molecular Gene Expression Gene Ontology Genome Internet Modeling and Simulation Molecular Sequence Annotation Phylogeny Protein Binding Species Specificity Transcription Factors - metabolism Transcription, Genetic Urochordata - genetics Vertebrates - genetics Web Browser
ISSN:	0305-1048, 1362-4962, 1362-4962
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Abstract	Abstract ANISEED (www.aniseed.cnrs.fr) is the main model organism database for tunicates, the sister-group of vertebrates. This release gives access to annotated genomes, gene expression patterns, and anatomical descriptions for nine ascidian species. It provides increased integration with external molecular and taxonomy databases, better support for epigenomics datasets, in particular RNA-seq, ChIP-seq and SELEX-seq, and features novel interactive interfaces for existing and novel datatypes. In particular, the cross-species navigation and comparison is enhanced through a novel taxonomy section describing each represented species and through the implementation of interactive phylogenetic gene trees for 60% of tunicate genes. The gene expression section displays the results of RNA-seq experiments for the three major model species of solitary ascidians. Gene expression is controlled by the binding of transcription factors to cis-regulatory sequences. A high-resolution description of the DNA-binding specificity for 131 Ciona robusta (formerly C. intestinalis type A) transcription factors by SELEX-seq is provided and used to map candidate binding sites across the Ciona robusta and Phallusia mammillata genomes. Finally, use of a WashU Epigenome browser enhances genome navigation, while a Genomicus server was set up to explore microsynteny relationships within tunicates and with vertebrates, Amphioxus, echinoderms and hemichordates.
AbstractList	ANISEED (www.aniseed.cnrs.fr) is the main model organism database for tunicates, the sister-group of vertebrates. This release gives access to annotated genomes, gene expression patterns, and anatomical descriptions for nine ascidian species. It provides increased integration with external molecular and taxonomy databases, better support for epigenomics datasets, in particular RNA-seq, ChIP-seq and SELEX-seq, and features novel interactive interfaces for existing and novel datatypes. In particular, the cross-species navigation and comparison is enhanced through a novel taxonomy section describing each represented species and through the implementation of interactive phylogenetic gene trees for 60% of tunicate genes. The gene expression section displays the results of RNA-seq experiments for the three major model species of solitary ascidians. Gene expression is controlled by the binding of transcription factors to cis-regulatory sequences. A high-resolution description of the DNA-binding specificity for 131 Ciona robusta (formerly C. intestinalis type A) transcription factors by SELEX-seq is provided and used to map candidate binding sites across the Ciona robusta and Phallusia mammillata genomes. Finally, use of a WashU Epigenome browser enhances genome navigation, while a Genomicus server was set up to explore microsynteny relationships within tunicates and with vertebrates, Amphioxus, echinoderms and hemichordates. ANISEED (www.aniseed.cnrs.fr) is the main model organism database for tunicates, the sister-group of vertebrates. This release gives access to annotated genomes, gene expression patterns, and anatomical descriptions for nine ascidian species. It provides increased integration with external molecular and taxonomy databases, better support for epigenomics datasets, in particular RNA-seq, ChIP-seq and SELEX-seq, and features novel interactive interfaces for existing and novel datatypes. In particular, the cross-species navigation and comparison is enhanced through a novel taxonomy section describing each represented species and through the implementation of interactive phylogenetic gene trees for 60% of tunicate genes. The gene expression section displays the results of RNA-seq experiments for the three major model species of solitary ascidians. Gene expression is controlled by the binding of transcription factors to cis-regulatory sequences. A high-resolution description of the DNA-binding specificity for 131 Ciona robusta (formerly C. intestinalis type A) transcription factors by SELEX-seq is provided and used to map candidate binding sites across the Ciona robusta and Phallusia mammillata genomes. Finally, use of a WashU Epigenome browser enhances genome navigation, while a Genomicus server was set up to explore microsynteny relationships within tunicates and with vertebrates, Amphioxus, echinoderms and hemichordates.ANISEED (www.aniseed.cnrs.fr) is the main model organism database for tunicates, the sister-group of vertebrates. This release gives access to annotated genomes, gene expression patterns, and anatomical descriptions for nine ascidian species. It provides increased integration with external molecular and taxonomy databases, better support for epigenomics datasets, in particular RNA-seq, ChIP-seq and SELEX-seq, and features novel interactive interfaces for existing and novel datatypes. In particular, the cross-species navigation and comparison is enhanced through a novel taxonomy section describing each represented species and through the implementation of interactive phylogenetic gene trees for 60% of tunicate genes. The gene expression section displays the results of RNA-seq experiments for the three major model species of solitary ascidians. Gene expression is controlled by the binding of transcription factors to cis-regulatory sequences. A high-resolution description of the DNA-binding specificity for 131 Ciona robusta (formerly C. intestinalis type A) transcription factors by SELEX-seq is provided and used to map candidate binding sites across the Ciona robusta and Phallusia mammillata genomes. Finally, use of a WashU Epigenome browser enhances genome navigation, while a Genomicus server was set up to explore microsynteny relationships within tunicates and with vertebrates, Amphioxus, echinoderms and hemichordates. Abstract ANISEED (www.aniseed.cnrs.fr) is the main model organism database for tunicates, the sister-group of vertebrates. This release gives access to annotated genomes, gene expression patterns, and anatomical descriptions for nine ascidian species. It provides increased integration with external molecular and taxonomy databases, better support for epigenomics datasets, in particular RNA-seq, ChIP-seq and SELEX-seq, and features novel interactive interfaces for existing and novel datatypes. In particular, the cross-species navigation and comparison is enhanced through a novel taxonomy section describing each represented species and through the implementation of interactive phylogenetic gene trees for 60% of tunicate genes. The gene expression section displays the results of RNA-seq experiments for the three major model species of solitary ascidians. Gene expression is controlled by the binding of transcription factors to cis-regulatory sequences. A high-resolution description of the DNA-binding specificity for 131 Ciona robusta (formerly C. intestinalis type A) transcription factors by SELEX-seq is provided and used to map candidate binding sites across the Ciona robusta and Phallusia mammillata genomes. Finally, use of a WashU Epigenome browser enhances genome navigation, while a Genomicus server was set up to explore microsynteny relationships within tunicates and with vertebrates, Amphioxus, echinoderms and hemichordates.
Author	Swalla, Billie Cambillau, Christian Christiaen, Lionel Simion, Paul Mendez, Mickael Gineste, Mathieu Piette, Jacques Volff, Jean-Nicolas Stolfi, Alberto Kusakabe, Takehiro Nakai, Kenta Nitta, Kazuhiro R Brozovic, Matija Roberge, Alexis Dardaillon, Justine Satou, Yutaka Veeman, Michael Dumollard, Rémi Brown, C Titus Faure, Emmanuel Naville, Magali Aicha, Sameh Ben Jacox, Edwin Delsuc, Frédéric Reeves, Wendy Louis, Alexandra Lemaire, Patrick Yokomori, Rui Fagotto, Marie Dauga, Delphine Bellec, Maelle Vincentelli, Renaud Douzery, Emmanuel Guéroult-Bellone, Marion Dantec, Christelle Haeussler, Maximilian Lowe, Elijah K Scornavacca, Céline Nishida, Hiroki
AuthorAffiliation	Bioself Communication; 28 rue de la Bibliothèque, F-13001 Marseille, France Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan IBDM, Aix-Marseille Université, CNRS, Campus de Luminy, Case 907; 163 Avenue de Luminy, F-13288 Marseille Cedex 9, France Division of Biology, Kansas State University, Manhattan, Kansas Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy New York University, Center for Developmental Genetics, Department of Biology, 1009 Silver Center, 100 Washington Square East, New York City, NY10003, USA Team VORTEX, Institut de Recherche en Informatique de Toulouse, Universities Toulouse I and III, CNRS, INPT, ENSEEIHT; 2 rue Camichel, BP 7122, F-31071 Toulouse Cedex 7, France Institut de Biologie Computationnelle, Université de Montpellier, Montpellier, France Population Health and Reproduction, UC Davis, Davis, CA 95616, USA I
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BackLink	https://www.ncbi.nlm.nih.gov/pubmed/29149270$$D View this record in MEDLINE/PubMed https://hal.science/hal-01636650$$DView record in HAL
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ContentType	Journal Article
Copyright	The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research. 2018 The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research. licence_http://creativecommons.org/publicdomain/zero
Copyright_xml	– notice: The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research. 2018 – notice: The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research. – notice: licence_http://creativecommons.org/publicdomain/zero
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Snippet	Abstract ANISEED (www.aniseed.cnrs.fr) is the main model organism database for tunicates, the sister-group of vertebrates. This release gives access to... ANISEED (www.aniseed.cnrs.fr) is the main model organism database for tunicates, the sister-group of vertebrates. This release gives access to annotated...
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SubjectTerms	Animals Biological Evolution Ciona intestinalis - genetics Computer Science Data Mining Database Issue Databases, Genetic Datasets as Topic DNA - metabolism Evolution, Molecular Gene Expression Gene Ontology Genome Internet Modeling and Simulation Molecular Sequence Annotation Phylogeny Protein Binding Species Specificity Transcription Factors - metabolism Transcription, Genetic Urochordata - genetics Vertebrates - genetics Web Browser
Title	ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets
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